Status
Assembly v2 (April 2013) is an assembly of Solexa gDNA reads using AllPathsLG improved by PacBio reads using PBJelly.
Summary statistics for the Hypoxylon sp. EC38 v3.0 release
are below.
| Genome Assembly | |
| Genome Assembly size (Mbp} | 47.72 |
| Sequencing read coverage depth | 116.1x |
| # of contigs | 582 |
| # of scaffolds | 288 |
| # of scaffolds >= 2Kbp | 225 |
| Scaffold N50 | 16 |
| Scaffold L50 (Mbp) | 0.99 |
| # of gaps | 294 |
| % of scaffold length in gaps | 0.3% |
| Three largest Scaffolds (Mbp) | 3.25, 2.46, 1.96 |
| ESTs | Data set | # sequences total | # mapped to genome | % mapped to genome |
| Other | Rnnotator_contigs | 38317 | 35866 | 93.6% |
| Gene Models | FilteredModels1 | |
| length (bp) of: | average | median |
| gene | 1793 | 1535 |
| transcript | 1580 | 1377 |
| exon | 539 | 324 |
| intron | 112 | 64 |
| description: | ||
| protein length (aa) | 458 | 381 |
| exons per gene | 2.93 | 2 |
| # of gene models | 12534 |
Collaborators
- DOE Joint Genome Institute
- Blake Simmons at DOE Joint BioEnergy Institute and Sandia National Laboratories
- John Gladden at DOE Joint BioEnergy Institute and Sandia Labs.
Genome Reference(s)
Please cite the following publication(s) if you use the data from this genome in your research:
Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM
Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.
Appl Microbiol Biotechnol. 2017 Mar;101(6):2603-2618. doi: 10.1007/s00253-017-8091-1
Wu W, Davis RW, Tran-Gyamfi MB, Kuo A, LaButti K, Mihaltcheva S, Hundley H, Chovatia M, Lindquist E, Barry K, Grigoriev IV, Henrissat B, Gladden JM
Characterization of four endophytic fungi as potential consolidated bioprocessing hosts for conversion of lignocellulose into advanced biofuels.
Appl Microbiol Biotechnol. 2017 Mar;101(6):2603-2618. doi: 10.1007/s00253-017-8091-1
Funding
The work conducted by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
